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Wrong rotatable bond in pdbqt format results in re-docking (sampling) failure #2433
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Thanks for opening your first issue here! Be sure to follow the issue template! |
It looks as though the pdbqt rotatable-bond perception function excludes amidine bond patterns (N=C-N), which appears to be the bond that's excluded from the pdbqt tree. |
I agree with you. |
Is there a target release to fix this issue ? When will the fix be ready ? Thanks a lot |
Add this line into the function "static bool IsImide(OBBond* querybond)" |
Environment Information
Open Babel version: 3.1.1
Operating system and version: Centos 7.4
Expected Behavior
Example 1. C1(NC2=NC(C3=CN=CC=C3)=CC=N2)=CC=CC=C1
As for example 1 molecule, obabel give a PDBQT file with 2 rotatable bond instead of 3. The correct one looks like as following:
Actual Behavior
The torsions in PDBQT file did not include bond C_2-N_3. This will result in docking failure. Let me show you an redocking failure: openbabel_2433
Steps to Reproduce
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